First one I thought of was Suki mo Kirai mo Jikangai. Also The Uke in Virgin Love, but theres a whole series by Fujisaki Kou and that is the 3rd story in the series (alot of people don't like the artwork but I loved it and stories were good also). I think there was also a scene in Hidoku Shinaide where Nemugasa has an issue. I'd be happy to read any other storeies if anybody else has ideas! :)
I read this just yesterday, it's very cuteヾ(❀╹◡╹)ﾉ~
http://www.mangago.zone/read-manga/hana_no_mizo_shiru/
In my favorite manga lists, there're 2 Uke having breathing problem (asthma) when they're too tense. Your request makes me wanna re-read
http://www.mangago.zone/read-manga/hana_no_mizo_shiru/ - Prequel
http://www.mangago.zone/read-manga/hana_no_migoro_ni/ - Sequel
http://www.mangago.zone/read-manga/suki_mo_kirai_mo_jikangai/
yaoi manga with hyperventilating uke